But then why did they program the nanites to take out all of a plane's systems except for its running lights so that you could just so happen to see them fall out of the sky at night when the blackout hit?
Meh, you're nitpicking. The Walking Dead is a great show and desipite that there are easy to nitpick inconsistent elements. e.g.
1. How is the grass mown at the prison?
2. How do they manage to keep the car they drive around clean all the time? Why would they bother to clean it?
The same kind of nitpicks we cal also find in Star Trek or any other show that uses plot devices to make the story compelling or visually exciting.